Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity.

Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic "isoprenol pathways," which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non-natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non-natural substrates using the IPK homolog from Thermococcus paralvinellae (TcpIPK). Four such structures were solved, each bound to a different non-natural alkyl-P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures of TcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl-P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures of TcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non-natural substrates.

Histochemical studies on the distribution and accumulation of trans-polyisoprene in the rubber-producing plant Eucommia ulmoides.

Eucommia ulmoides rubber (EUR) is a high-quality natural rubber resource, which can be extracted from different organs of the Eucommia ulmoides tree. In this study, EUR was isolated from the leaves, barks, and pericarps, and the structural characteristics and physicochemical properties of EUR were systematically determined. The accumulation and distribution of EUR in different tissues were assessed through in situ observations combined with cellular and subcellular scales. The preliminary analyses indicated that the variations in the physicochemical properties of EUR across different tissues were associated with its accumulation microstructure. Further analyses by SEM and TEM showed that the initial cell differentiation and fusion resulted in the formation of tubular structures without any nucleus. A limited number of rubber particles were generated within the cytoplasm, concurrent with aggregation and fusion. Eventually, rubber particles filled the entire cytoplasm, and organelles disappeared to form highly aggregated filamentous structures. In addition, the number and area of EUR-containing cells were closely related to the organization sizes of barks and leaves. This study provided valuable insights into Eucommia ulmoides histology and the rubber industry.

Kinetic study of isoprene hydroxy hydroperoxide radicals reacting with sulphur dioxide and their global-scale impact on sulphate formation.

Isoprene is the most relevant volatile organic compound emitted during the biosynthesis of metabolism processes. The oxidation of isoprene by a hydroxy radical (OH) is one of the main consumption schemes that generate six isomers of isoprene hydroxy hydroperoxide radicals (ISOPOOs). In this study, the rate constants of ISOPOOs + sulphur dioxide (SO2) reactions that eventually generate sulphur trioxide (SO3), the precursor of sulphate aerosol (SO42-(p)), are determined using microcanonical kinetic theories coupled with molecular structures and energies estimated by quantum chemical calculations. The results show that the reaction rates range from 10-27 to 10-20 cm3 molecule-1 s-1, depending on the atmospheric temperature and structure of the six ISOPOO isomers. The effect of SO3 formation from SO2 oxidation by ISOPOOs on the atmosphere is evaluated by a global chemical transport model, along with the rate constants obtained from microcanonical kinetic theories. The results show that SO3 formation is enhanced in regions with high SO2 or low nitrogen oxide (NO), such as China, the Middle East, and Amazon rainforests. However, the production rates of SO3 formation by ISOPOOs + SO2 reactions are eight orders of magnitude lower than that from the OH + SO2 reaction. This is indicative of SO42-(p) formation from the direct oxidation of SO2 by ISOPOOs, which is almost negligible in the atmosphere. The results of this study entail a detailed analysis of SO3 formation from gas-phase reactions of isoprene-derived products.

Computational investigation of cis-1,4-polyisoprene binding to the latex-clearing protein LcpK30.

Latex clearing proteins (Lcps) catalyze the oxidative cleavage of the C = C bonds in cis-1,4-polyisoprene (natural rubber), producing oligomeric compounds that can be repurposed to other materials. The active catalytic site of Lcps is buried inside the protein structure, thus raising the question of how the large hydrophobic rubber chains can access the catalytic center. To improve our understanding of hydrophobic polymeric substrate binding to Lcps and subsequent catalysis, we investigated the interaction of a substrate model containing ten carbon-carbon double bonds with the structurally characterized LcpK30, using multiple computational tools. Prediction of the putative tunnels and cavities in the LcpK30 structure, using CAVER-Pymol plugin 3.0.3, fpocket and Molecular Dynamic (MD) simulations provided valuable insights on how substrate enters from the surface to the buried active site. Two dominant tunnels were discovered that provided feasible routes for substrate binding, and the presence of two hydrophobic pockets was predicted near the heme cofactor. The larger of these pockets is likely to accommodate the substrate and to determine the size distribution of the oligomers. Protein-ligand docking was carried out using GOLD software to predict the conformations and interactions of the substrate within the protein active site. Deeper insight into the protein-substrate interactions, including close-contacts, binding energies and potential cleavage sites in the cis-1,4-polyisoprene, were obtained from MD simulations. Our findings provide further justification that the protein-substrate complexation in LcpK30 is mainly driven by the hydrophobic interactions accompanied by mutual conformational changes of both molecules. Two potential binding modes were identified, with the substrate in either extended or folded conformations. Whilst binding in the extended conformation was most favorable, the folded conformation suggested a preference for cleavage of a central double bond, leading to a preference for oligomers with 5 to 6 C = C bonds. The results provide insight into further enzyme engineering studies to improve catalytic activity and diversify the substrate and product scope of Lcps.

Clinical relevance of trans 1.4-polyisoprene aging degradation on the longevity of root canal treatment

This in vivo study investigated the time of degradation of root filling material (trans 1,4-polyisoprene) retrieved from endodontically treated teeth and correlated the occurrence of degradation with the longevity of endodontics. Thirty-six root-filled teeth with different filling times (2 to 30 years) and with and without periapical lesions were selected. All teeth presented clinical indication for root canal retreatment. The association among filling time, presence of periapical lesion and root filling material degradation was investigated. Root filling samples were retrieved from the root canals using a Hedströ m file without solvent. The trans 1,4-polyisoprene was isolated by root filling solubilization in chloroform followed by filtration and centrifugation. GPC and FT-IR were the analytical techniques utilized. Degradation of trans 1,4-polyisoprene occurred with time, as a slow process. It is an oxidative process, and production of carboxyl and hydroxyl groups in the residual polymer were observed. Statistically significant decrease of molar mass was observed after 5 (p=0.0001) and 15 (p=0.01) years in teeth with and without periapical lesion, respectively. Bacteria participated in polymer degradation. Gutta-percha aging was proven an important factor for the long-term success of endodontic treatment. The findings of the present study showed that, after 15 years, polymer weight loss may decrease the capacity of the filling mass to seal the root canal space and prevent re-infection, thus compromising significantly the longevity of root canal therapy.

Este estudo in vivo avaliou a degradação do material obturador e a influência deste fator na longevidade do tratamento endodôntico. Foram selecionados 36 pacientes (3-30 anos) com canais tratados endodonticamente, com e sem lesões periapicais, e indicação de retratamento endodôntico. Foi investigada a associação entre o tempo de tratamento, presença de lesão periapical e a degradação do material obturador. O material obturador foi removido com uma lima Hedströ em sem uso de solvente. O polímero trans 1,4- poliisopreno foi isolado do material obturador através de solubilização em clorofórmio, seguido de filtragem e centrifugação. GPC e FT-IR foram os métodos analíticos utilizados. A degradação do trans 1,4- poliisopreno foi observada com o tempo, sendo um processo lento e oxidativo, com formação de grupos carboxílicos e hidroxilas no polímero residual. Após 5 (p=0,0001) e 15 (p=0,01) anos, em dentes com e sem lesões periapicais, respectivamente, houve decréscimos significantes na massa molar do material obturador. A infecção bacteriana participa no processo de degradação do polímero. O envelhecimento da guta-percha é um fator que influencia o sucesso a longo prazo do tratamento endodôntico. Após 15 anos, a longevidade do tratamento pode ser significantemente afetada pela redução da capacidade de selamento causada pela perda de massa molar do polímero, permitindo a reinfecção do sistema de canais radiculares.